Molecular Insights into Geometric and Electrophoretic Effects on DNA Translocation Speed Through Graphene Nanoslit Sensor

2021 ◽  
Author(s):  
Changxiong Huang ◽  
Xiaohong Zhu ◽  
Zhen Li ◽  
Xinyao Ma ◽  
Na Li ◽  
...  
Keyword(s):  
Dna Translocation ◽  
Translocation Speed

scholarly journals Osmotically Driven and Detected DNA Translocations

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Angus McMullen ◽  
George Araujo ◽  
Michele Winter ◽  
Derek Stein
Keyword(s):  
Solid State ◽  
Salinity Gradient ◽  
Ionic Current ◽  
Dna Translocation ◽  
Dna Molecule ◽  
Salinity Gradients ◽  
Current Change ◽  
Theoretical Analyses ◽  
Translocation Speed

Abstract A salinity gradient propels a DNA molecule through a solid-state nanopore and generates an ionic current whose change allows for the detection of the translocation. Measurements and theoretical analyses reveal the role of diffusio-osmosis in driving these phenomena: After accounting for known salinity-dependent electrode effects, the measured current change caused by the presence of a DNA molecule inside the nanopore and the DNA translocation speed through it both increase with the magnitude of the applied salinity gradients. The effects are consistent with the theory of diffuisio-osmosis and strong enough to enable DNA translocations to overcome an applied retarding potential of tens of millivolts. This work illustrates how salinity gradients can be used to power and operate a nanopore sensor.

Molecular Dynamics Study of DNA Translocation Through Graphene Nanopores With Controllable Speed

2015 ◽  
Author(s):  
Kun Li ◽  
Wei Si ◽  
Jingjie Sha ◽  
Yunfei Chen
Keyword(s):  
Molecular Dynamics ◽  
Ionic Current ◽  
Ionic Currents ◽  
Dna Bases ◽  
Dna Translocation ◽  
Dna Molecule ◽  
Long Time ◽  
Pulling Force ◽  
Current Blockage ◽  
Translocation Speed

All-atom steered molecular dynamics (SMD) simulations provide the means to study the single-stranded DNA (ssDNA) translocation through graphene nanopores at a controllable speed. The ssDNA is pulled by an elastic force similar to the manipulation by an AFM tip. At the same time, an electric field is applied across the reservoir along the direction of the pulling force, in order to hold the ssDNA strand taut and drive the ions in the solutions through the nanopore. By monitoring and analyzing the average ionic current blockage of poly(dA)10, poly(dC)10, poly(dG)10 and poly(dT)10, it is found that one can indeed discriminate the different DNA bases from each other by holding each nucleotide in the pore for sufficiently long time. It is obtained the average blocked ionic currents can be listed, in a increasing order, as IG<IA<IT, which is almost in agreement with the order of sizes of the four nucleotides (VG>VA>VT>VC), apart from C. The results indicate that physical occupancy of the nucleotide plays the major role in affecting average blocked ionic current when the DNA translocation speed is effectively slowed down. This work provides a clue for the further investigation to realize the discrimination of the four nucleotides by the method of actively controlling DNA molecule translocation speed through the nanopores.

Ionic liquid prolongs DNA translocation through graphene nanopores

RSC Advances ◽  
2016 ◽  
Vol 6 (51) ◽  
pp. 46019-46029 ◽  
Author(s):  
Mandar Kulkarni ◽  
Arnab Mukherjee
Keyword(s):  
Ionic Liquid ◽  
Dna Translocation ◽  
Translocation Speed ◽  
Graphene Nanopore

Ionic liquid molecules interact strongly with DNA and effectively reduce its translocation speed via graphene nanopore.

scholarly journals Slowing Down DNA Translocation Speed thorough a Nanopore by a Nanofibre Meshed Layer

2018 ◽  
Vol 114 (3) ◽  
pp. 180a
Author(s):  
Daming Zhou ◽  
Yue Zhao ◽  
Enling Tian ◽  
Deqiang Wang
Keyword(s):  
Dna Translocation ◽  
Slowing Down ◽  
Translocation Speed

scholarly journals Controlling DNA Translocation Through Solid-state Nanopores

2020 ◽  
Vol 15 (1) ◽  
Author(s):  
Zhishan Yuan ◽  
Youming Liu ◽  
Min Dai ◽  
Xin Yi ◽  
Chengyong Wang
Keyword(s):  
Solid State ◽  
Dna Translocation

scholarly journals Sophisticated Conversations between Chromatin and Chromatin Remodelers, and Dissonances in Cancer

2021 ◽  
Vol 22 (11) ◽  
pp. 5578
Author(s):  
Cedric R. Clapier
Keyword(s):  
Gene Expression ◽  
Regulation Of Gene Expression ◽  
Structural Diversity ◽  
Nucleosome Positioning ◽  
Basic Mechanism ◽  
Progressive Increase ◽  
Chromatin Organization ◽  
Dna Translocation ◽  
Dynamic Regulation ◽  
Cooperative Action

The establishment and maintenance of genome packaging into chromatin contribute to define specific cellular identity and function. Dynamic regulation of chromatin organization and nucleosome positioning are critical to all DNA transactions—in particular, the regulation of gene expression—and involve the cooperative action of sequence-specific DNA-binding factors, histone modifying enzymes, and remodelers. Remodelers are molecular machines that generate various chromatin landscapes, adjust nucleosome positioning, and alter DNA accessibility by using ATP binding and hydrolysis to perform DNA translocation, which is highly regulated through sophisticated structural and functional conversations with nucleosomes. In this review, I first present the functional and structural diversity of remodelers, while emphasizing the basic mechanism of DNA translocation, the common regulatory aspects, and the hand-in-hand progressive increase in complexity of the regulatory conversations between remodelers and nucleosomes that accompanies the increase in challenges of remodeling processes. Next, I examine how, through nucleosome positioning, remodelers guide the regulation of gene expression. Finally, I explore various aspects of how alterations/mutations in remodelers introduce dissonance into the conversations between remodelers and nucleosomes, modify chromatin organization, and contribute to oncogenesis.

scholarly journals DNA Translocation through Graphene Nanopores

Nano Letters ◽  
2010 ◽  
Vol 10 (8) ◽  
pp. 3163-3167 ◽  
Author(s):  
Grégory F. Schneider ◽  
Stefan W. Kowalczyk ◽  
Victor E. Calado ◽  
Grégory Pandraud ◽  
Henny W. Zandbergen ◽  
...  
Keyword(s):  
Dna Translocation
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